PHYSIOLOGICAL AND TRANSCRIPTOMIC ASPECTS OF ADAPTATION TO EXTREME ENVIRONMENTS by COURTNEY NICOLE PASSOW B.S., Texas A&M University, 2011 AN ABSTRACT OF A DISSERTATION submitted in partial fulfillment of the requirements for the degree DOCTOR OF PHILOSOPHY Division of Biology College of Arts and Sciences KANSAS STATE UNIVERSITY Manhattan, Kansas 2016 Abstract Extremophiles are organisms with the ability to survive in environments characterized by strong physicochemical stressors lethal to most other organisms, providing excellent models to further our understanding of life’s capacities and limitations to deal with far-from-average conditions. I studied how physiological processes varied among fish residing in starkly different environmental conditions to understand how organisms cope with extreme environments and disentangle the roles of short-term plastic responses and evolved population differences in shaping physiological responses. I used the Poecilia mexicana model, a series of extremophile fish populations that has colonized toxic hydrogen sulfide (H2S) rich springs and caves, to address three major objectives: (1) I investigated the energetic consequences of life in extreme environments and tested whether predicted reductions in organismal energy demands evolved repeatedly along replicated environmental gradients. (2) I characterized variation in gene expression among populations and organs to test for interactive effects between different stressors and identify potential physiological mechanisms underlying adaptation to H2S and cave environments. (3) I conducted common garden and H2S-exposure experiments to test how evolutionary change and plasticity interact to shape variation in gene expression observed in nature. To address these objectives, I measured variation in metabolic physiology and quantified variation in physiological processes through genome-wide gene expression analyses. I found that adaptation to extreme environments directly impacts energy metabolism, with fish living in extreme environments consistently expending less energy overall. Reductions in energy demand have evolved in convergence and were primarily mediated through a life history shift (reduction in body mass). The quantification of gene expression across divergent habitats and organs revealed organ-specific physiological responses in H2S-rich and cave habitats. Gene expression variation in the relevant genes was primarily shaped by evolutionary change in gene regulation, and ancestral plastic responses play a minor role in causing the observed expression differences between replicated sulfidic and nonsulfidic populations in nature. Overall, my research has implications for understanding the capacities and constraints that shape life in extreme environments and aids in our understanding of modifications in physiological pathways mediating adaptation to elevated H2S and perpetual darkness. PHYSIOLOGICAL AND TRANSCRIPTOMIC ASPECTS OF ADAPTATION TO EXTREME ENVIRONMENTS by COURTNEY NICOLE PASSOW B.S., Texas A&M University, 2011 A DISSERTATION submitted in partial fulfillment of the requirements for the degree DOCTOR OF PHILOSOPHY Division of Biology College of Arts and Sciences KANSAS STATE UNIVERSITY Manhattan, Kansas 2016 Approved by: Major Professor Michael Tobler Copyright COURTNEY NICOLE PASSOW 2016 Abstract Extremophiles are organisms with the ability to survive in environments characterized by strong physicochemical stressors lethal to most other organisms, providing excellent models to further our understanding of life’s capacities and limitations to deal with far-from-average conditions. I studied how physiological processes varied among fish residing in starkly different environmental conditions to understand how organisms cope with extreme environments and disentangle the roles of short-term plastic responses and evolved population differences in shaping physiological responses. I used the Poecilia mexicana model, a series of extremophile fish populations that has colonized toxic hydrogen sulfide (H2S) rich springs and caves, to address three major objectives: (1) I investigated the energetic consequences of life in extreme environments and tested whether predicted reductions in organismal energy demands evolved repeatedly along replicated environmental gradients. (2) I characterized variation in gene expression among populations and organs to test for interactive effects between different stressors and identify potential physiological mechanisms underlying adaptation to H2S and cave environments. (3) I conducted common garden and H2S-exposure experiments to test how evolutionary change and plasticity interact to shape variation in gene expression observed in nature. To address these objectives, I measured variation in metabolic physiology and quantified variation in physiological processes through genome-wide gene expression analyses. I found that adaptation to extreme environments directly impacts energy metabolism, with fish living in extreme environments consistently expending less energy overall. Reductions in energy demand have evolved in convergence and were primarily mediated through a life history shift (reduction in body mass). The quantification of gene expression across divergent habitats and organs revealed organ-specific physiological responses in H2S-rich and cave habitats. Gene expression variation in the relevant genes was primarily shaped by evolutionary change in gene regulation, and ancestral plastic responses play a minor role in causing the observed expression differences between replicated sulfidic and nonsulfidic populations in nature. Overall, my research has implications for understanding the capacities and constraints that shape life in extreme environments and aids in our understanding of modifications in physiological pathways mediating adaptation to elevated H2S and perpetual darkness. Table of Contents List of Figures ................................................................................................................................. x List of Tables ................................................................................................................................. xi Acknowledgements ....................................................................................................................... xii Dedication ..................................................................................................................................... xv Preface.......................................................................................................................................... xvi Chapter 1 - Reduction of energetic demands through modification of body size and routine metabolic rates in extremophile fish1 ...................................................................................... 1 Abstract ....................................................................................................................................... 1 Introduction ................................................................................................................................. 2 Material and Methods ................................................................................................................. 6 Results ....................................................................................................................................... 11 Discussion ................................................................................................................................. 13 Figures ...................................................................................................................................... 19 Tables ........................................................................................................................................ 22 Chapter 2 - Convergent evolution of reduced energy demands in extremophile fish .................. 26 Abstract ..................................................................................................................................... 26 Introduction ............................................................................................................................... 27 Materials and methods .............................................................................................................. 29 Results ....................................................................................................................................... 33 Discussion ................................................................................................................................. 34 Figures ...................................................................................................................................... 39 Tables ........................................................................................................................................ 41 Chapter 3 - Tissue-specific responses to toxic hydrogen sulfide and permanent darkness in livebearing fishes ................................................................................................................... 45 Abstract ..................................................................................................................................... 45 Introduction ............................................................................................................................... 46 Methods ...................................................................................................................................